What is the trade-off between a higher megapixels camera versus more powerful focal lengths

What do you mean by a more powerful focal length? A shorter focal length results in a more wide angled image, so a larger footprint on the ground. More wideangled lenses also have a better base-height ratio (better intersection angles of measurements, so in general a better height accuracy). More megapixels result in a smaller ground sample distance...so more details you'll see in the images. Smaller ground sample distance means more precise measurements (e.g. positional accuracy of georeferencing typically is 0.5 times the ground sample distance).